MHap Analysis Report: Genetic Relatedness (IBD) and Tranmission

library(dplyr)
library(magrittr)
load(params$RData_image)

plot_relatedness_distribution_within$plot

Figure 1: IBD distribution within sites

plot_frac_highly_related_within$plot

Figure 2: Frequency of highly related among sites

if(!is.na(Variable2)){plot_frac_highly_related_overtime_within$plot_frac_highly_related}

Figure 2: Frequency of highly related between sites over time

Pairwise relatedness comparisons between categories of Variable1

plot_relatedness_distribution_within$relatedness %>%
  DT::datatable(extensions = 'Buttons',
                options = list(dom = 'Blfrtip',
                  buttons = c('csv', 'excel')))

Fraction of highly related comparisons between categories of Variable1

plot_frac_highly_related_within$highly_related_table %>%
  DT::datatable(extensions = 'Buttons',
                options = list(dom = 'Blfrtip',
                  buttons = c('csv', 'excel')))

Fraction of highly related comparisons between categories of Variable1 over Variable2

if(!is.na(Variable2)){plot_frac_highly_related_overtime_within$frac_highly_related %>%
  DT::datatable(extensions = 'Buttons',
                options = list(dom = 'Blfrtip',
                  buttons = c('csv', 'excel')))}